I have glasses because they were included in TrackMania United Forever (I think).

However, at least with TrackMania the effect really doesn't work all that well. Moving your head completely ruins the effect and you constantly have to re-adjust the settings so that the stereo separation is set correctly according to your distance to the monitor.

Presumably the emulators all output to OpenGL or D3D to render and so we've been able to view them in 3D since day one (or 10 years ago, whichever comes later). I suspect the blocky low poly nature of N64 graphics would work rather well with 3D, building almost a papercraft/lego world to look into (Homeworld definitely got a lot out of 3D due to the quite basic nature of the 3D models). That said, I can't say I ever personally enjoyed an emulated game in 3D so maybe there is something funky that makes them hard to enable 3D mode with.

Shame the framerate limiting is completely off in this. For Mario Sunshine I have to manually force it to 25, but the FMV is 50 so that runs at half speed. If I turn off a couple of options it gets videos playing at the correct speed but the game slightly too slow (about 20fps).